Locus 4117

Sequence ID	X_DroMel_CAF1
Location	10,848,668 – 10,848,788
Length	120
Max. P	0.814364

overview

Window 4

Location	10,848,668 – 10,848,788
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	83.33
Mean single sequence MFE	-46.70
Consensus MFE	-31.79
Energy contribution	-30.72
Covariance contribution	-1.06
Combinations/Pair	1.33
Mean z-score	-1.98
Structure conservation index	0.68
SVM decision value	0.66
SVM RNA-class probability	0.814364
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10848668 120 + 22224390
UGUGUGGGCGAUGUGGCCAUCGUGUCUGGGUUAGACCGCAAAUGCAGACGGUUCGCCGGAGCGCGGAACAAGUUGUAAUUGUUGUUGGGAACGAACUAGGAUGGCAAACCCUGACCCACC
...(((((((..((.((((((..(((((.(((........))).)))))(((((((((.....)))(((((.......)))))........))))))..))))))..))..)).))))). ( -40.10)
>DroSec_CAF1 2669 120 + 1
UGUGUGGGCGAUGUGGCCAUCGUGUCUGGGUUAGACCGCAAAUGCAGACGGUUCGCCGGAGCGCGGAACAAGUAGUAAUUGUAGUUGGGAACAAACUAGGAUAGCAAGCCCUGACCCAUC
...((((((((((....))))))(((.(((((...((((....((...(((....)))..))))))........((.(((.((((((....).))))).))).)).))))).))))))). ( -40.90)
>DroSim_CAF1 2748 120 + 1
UGUGUGGGCGAUGUGGCCAUCGUGUCUGGGUUAGACCGCAAAUGCAGACGGUUCGCCGGAGCGCGGAACAAGUUGUAAUUGUAGUUGGGAACGAACUAGGAUGGCAAGCCCUGACCCAUC
...((((((((((....))))))(((.(((((...((((....((...(((....)))..)))))).......(((.(((.((((((....).))))).))).)))))))).))))))). ( -41.60)
>DroYak_CAF1 2751 120 + 1
UGGGGGGGGGGGGGGGGCCUUGGGUUUGGGGUUGGCCCCAAAAGCAGAAGGUUUGCCGACGGGGGGGACAAGUUGUAAUUGUUGUUGGAAAAGAAAUUGGGGGGCAAACCCCCCCCCCCC
.((((((((((((...((((((..(((((((....)))))))..)..((..(((.(((((((.((..((.....))..)).)))))))...)))..))..)))))...)))))))))))) ( -64.20)
>consensus
UGUGUGGGCGAUGUGGCCAUCGUGUCUGGGUUAGACCGCAAAUGCAGACGGUUCGCCGGAGCGCGGAACAAGUUGUAAUUGUAGUUGGGAACGAACUAGGAUGGCAAACCCUGACCCACC
...(((((((.....((((((.(((.((..((..((..(((.(((((...((((((......)).))))...))))).)))..))..))..)).)).).))))))......)).))))). (-31.79 = -30.72 +  -1.06)

alignment

secondary structure

dotplot

Window 5

Location	10,848,668 – 10,848,788
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	83.33
Mean single sequence MFE	-36.31
Consensus MFE	-25.41
Energy contribution	-24.73
Covariance contribution	-0.69
Combinations/Pair	1.25
Mean z-score	-1.83
Structure conservation index	0.70
SVM decision value	0.50
SVM RNA-class probability	0.760133
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10848668 120 - 22224390
GGUGGGUCAGGGUUUGCCAUCCUAGUUCGUUCCCAACAACAAUUACAACUUGUUCCGCGCUCCGGCGAACCGUCUGCAUUUGCGGUCUAACCCAGACACGAUGGCCACAUCGCCCACACA
.((((((...((((((((......(((.......)))(((((.......))))).........))))))))((((((....))((......))))))..((((....))))))))))... ( -35.70)
>DroSec_CAF1 2669 120 - 1
GAUGGGUCAGGGCUUGCUAUCCUAGUUUGUUCCCAACUACAAUUACUACUUGUUCCGCGCUCCGGCGAACCGUCUGCAUUUGCGGUCUAACCCAGACACGAUGGCCACAUCGCCCACACA
..((((((.(((..........((((((((........))))..)))).(((..((((((..(((....)))...))....))))..)))))).))).(((((....))))).))).... ( -28.50)
>DroSim_CAF1 2748 120 - 1
GAUGGGUCAGGGCUUGCCAUCCUAGUUCGUUCCCAACUACAAUUACAACUUGUUCCGCGCUCCGGCGAACCGUCUGCAUUUGCGGUCUAACCCAGACACGAUGGCCACAUCGCCCACACA
..(((((...(....((((((...(((((((.......((((.......))))..........))))))).((((((....))((......))))))..))))))..)...))))).... ( -29.83)
>DroYak_CAF1 2751 120 - 1
GGGGGGGGGGGGUUUGCCCCCCAAUUUCUUUUCCAACAACAAUUACAACUUGUCCCCCCCGUCGGCAAACCUUCUGCUUUUGGGGCCAACCCCAAACCCAAGGCCCCCCCCCCCCCCCCA
((((((((((((...(((...............................(((((.........)))))......((..(((((((....)))))))..)).)))...)))))))))))). ( -51.20)
>consensus
GAUGGGUCAGGGCUUGCCAUCCUAGUUCGUUCCCAACAACAAUUACAACUUGUUCCGCGCUCCGGCGAACCGUCUGCAUUUGCGGUCUAACCCAGACACGAUGGCCACAUCGCCCACACA
(((((((((.((((((((......(((.......))).((((.......))))..........))))))))...((..((((.((.....))))))..)).))))).))))......... (-25.41 = -24.73 +  -0.69)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:16:45 2006